SARS-CoV2 mutations and impact on mortality: observational study in a sub-saharan Africa hospital.

BACKGROUND: One year after the coronavirus disease 2019 (COVID-19) pandemic, the focus of attention has shifted to the emergence and spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs). The aim of the study was to assess the frequency of VOCs in patients followed for COVID-19 at Kinshasa university hospital (KUH) during the 3rd and 4th waves of the pandemic in Kinshasa. Hospital mortality was compared to that of the first two waves. METHOD: The present study included all patients in whom the diagnosis of SARS-CoV-2 infection was confirmed by the polymerase chain reaction (PCR). The laboratory team sequenced a subset of all SARS-CoV-2 positive samples with high viral loads define as Ct < 25 to ensure the chances to generate complete genome sequence. RNA extraction was performed using the Viral RNA Mini Kit (Qiagen). Depending on the platform, we used the iVar bioinformatics or artic environments to generate consensus genomes from the raw sequencing output in FASTQ format. RESULTS: During the study period, the original strain of the virus was no longer circulating. The Delta VOC was predominant from June (92%) until November 2021 (3rd wave). The Omicron VOC, which appeared in December 2021, became largely predominant one month later (96%) corresponding the 4th wave. In-hospital mortality associated with COVID-19 fell during the 2nd wave (7% vs. 21% 1st wave), had risen during the 3rd (16%) wave before falling again during the 4th wave (7%) (p < 0.001). CONCLUSION: The Delta (during the 3rd wave) and Omicron VOCs (during the 4th wave) were very predominant among patients followed for Covid-19 in our hospital. Contrary to data in the general population, hospital mortality associated with severe and critical forms of COVID-19 had increased during the 3rd wave of the pandemic in Kinshasa.

[Lesions on CT scan in patients hospitalized for coronavirus pneumonia during the first wave of the SARS-CoV-2 pandemic at the University Clinics in Kinshasa (DRC)]. / Lésions tomodensitométriques chez les patients hospitalisés pour pneumonie à COVID-19 lors de la première vague de la pandémie à SARS-CoV-2 aux Cliniques Universitaires de Kinshasa (RDC).

INTRODUCTION: the main purpose of this study is to describe chest computed tomography (CT) findings in 26 patients hospitalized with COVID-19 pneumonia during the first wave of the SARS-CoV-2 pandemic at the University Clinics in Kinshasa (UCK). METHODS: we conducted a descriptive study of chest CT findings in 26 patients hospitalized with coronavirus pneumonia at the UCK over a 9-month period, from March 17 to November 17, 2020. Hitachi - CT-scanner 16 slice was used in all our patients. After analyzing lesions, these were divided into lesions suggestive and non-suggestive of SARS-CoV-2 infection. RESULTS: the average age of patients was 53.02 years. Male sex was the most affected (76.9%). Respiratory distress was the most common clinical symptom (61.5%). Arterial hypertension and renal failure were the most common comorbidities (3O% and 6%). Bilateral ground-glass opacities, with a predominantly peripheral distribution, accounted for 69.2% of cases, followed by condensations (57.7%) and crazy paving (19.2%). Severe COVID-19 was most frequently found (34.61%). Distal and proximal pulmonary embolism was the most common complication (11.5%). Among the associated diseases, pleurisy and pulmonary PAH were most frequently found (30.8%). The majority of our patients had parenchymal lung lesions, corresponding to early-stage disease on CT (50%). CONCLUSION: at the UCK, during the first wave of SARS-CoV-2 pandemic, lesions on CT suggestive of COVID-19 were dominated by plaque-like ground-glass opacities, followed by nonsystematized parenchymatous condensations and crazy paving. The less observed atypical lesions consisted of unilateral, peribronchovascular pseudo-nodular condensations and infection in the remodeled lung. Severe COVID-19 was the most common CT finding. Proximal and distal pulmonary embolism was the most common complication. This study highlights that these findings are consistent with those reported in the literature.

The COVID-19 pandemic is deepening the health crisis in South Kivu, Democratic Republic of Congo.

OBJECTIVE: The outbreak of coronavirus disease 2019 (COVID-19) in South Kivu, Democratic Republic of Congo raised concerns regarding additional morbidity and mortality. Updating these indicators before a second wave is essential in order to prepare for additional help. METHODS: From mid-May to mid-December 2020, weekly surveys were undertaken in sampled streets from 10 health areas to quantify the use of barrier measures, and interview pedestrians about sickness and deaths in their households. Crude death rates (CDRs) were estimated. RESULTS: Minimal use or no use of face masks was observed in at least half of the streets. From May to December 2020, the number of suspected cases of COVID-19 increased six-fold (P < 0.05). Of deaths within 30 days preceding the interviews, 20% were considered to be related to COVID-19. The monthly CDRs at the beginning and end of the study were approximately 5 and 25 per 1000 population, respectively (P < 0.05); that is, annual CDRs of 60 and 260 per 1000 population, respectively. Thus, during the first wave, the estimated mortality rate increased by 50% compared with previous years, and increased at least four-fold by the end of 2020. CONCLUSION: Despite possible overestimations, the excess mortality in South Kivu is extremely concerning. This crisis calls for a rapid response and increased humanitarian assistance.

A dashboard for monitoring preventive measures in response to COVID-19 outbreak in the Democratic Republic of Congo.

BACKGROUND: In most health areas, an information system is necessary for an effective fight against COVID-19. Current methods for surveillance of diseases with epidemic potential do not include monitoring the adherence to preventive measures. Furthermore, modern data collection methods depend often on technologies (e.g., cameras or drones) that are hardly available in low-income countries. Simpler solutions could be just as effective. METHODS: A dashboard was used over a whole week to monitor preventive measures in Bukavu (DRC) by mid-May 2020. It was designed to collect from street passers-by information on the adherence to barrier measures, the level of awareness of these measures, the opinion on their usefulness, and the health status of people in the households. RESULTS: Creating a dashboard and collecting the necessary data proved feasible. The use of barrier measures was very limited and that of masks practically nil despite repeated recommendations from the health authorities. The end of each day was the worst moment due to clearly insufficient distancing. Barrier measures were significantly more used in areas where they were best known and most acknowledged. At the time of the study, there were few sick people and only rare severe cases were attributed to COVID-19. CONCLUSIONS: Creating COVID-19 situation dashboards in limited-resource metropoles is feasible. They give real-time access to data that help fight the epidemic. The findings of this pilot study call for a rapid community awareness actions to back national media-based prevention campaigns.